* For question 4 of the shared journal reflection, be careful in the way you state your answer. The profile and GO term p values do not refer to individual genes. The profile p value is a measure of the probability that you would see that many genes that fit that expression profile due to chance. The GO term p value is a measure of the probability that you would see that many genes in that profile associated with that GO term due to chance. The latter two p values are dealing with groups of genes, not individual genes. Also, the GO terms do not necessarily include transcription factors. There ''are'' GO terms specific for transcription, but most of the terms relate to other cellular processes.

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Week 12 Journal Feedback

Thank you for submitting your assignment on time.

The profile you chose, profile 9, has genes whose expression is slightly down-regulated at cold shock temperatures, and then return to no change versus the t0 control at the recovery temperatures. This means that the cell is down-regulating genes whose function is protein folding. Cold temperatures do not degrade proteins or denature them, so the cell actually does not need these functions. The cell might when the temperature goes up, so the expression levels are brought back up during recovery.

Week 12 Shared Journal

For question 4 of the shared journal reflection, be careful in the way you state your answer. The profile and GO term p values do not refer to individual genes. The profile p value is a measure of the probability that you would see that many genes that fit that expression profile due to chance. The GO term p value is a measure of the probability that you would see that many genes in that profile associated with that GO term due to chance. The latter two p values are dealing with groups of genes, not individual genes. Also, the GO terms do not necessarily include transcription factors. There are GO terms specific for transcription, but most of the terms relate to other cellular processes.

Week 9 Spreadsheet Feedback

I've reviewed the spreadsheet that you submitted for the Week 9 assignment. There is an error on the calcuations you made on the "scaled_centered" worksheet that affects all of the downstream calculations. You used the function "STDEVP" instead of "STDEV" for calculating the standard deviation of the log fold changes on this chip. The "STDEV" function should only be used when you have data for the entire population, not a sample of the population, which is what we have. You will need to make this correction before going on to the Week 12 assignment.

Week 1 Journal Feedback

Thank you for submitting your assignment on time.

There are a few of things that you need to fix on your individual user page and shared journal page. Please make these changes by next week's journal deadline (midnight, February 8) to earn back the points you missed on this assignment.

You need to put the complete street address for your box at LMU.

On the Week 1 shared journal page, put the link to your user page underneath the header for your section.

You are writing something in the summary field consistently; remember, the goal is to fill it out every time you make a change.

Your external link needs a label. What you did works, but it would be better to use the complete wiki syntax. I.e., use [http://www.lmu.edu LMU], which looks like this: LMU, instead of just [1].

While you have created a template and used it, it could be organized better. Use a bulleted or numbered list to organize your links. While it looks like you used line breaks to separate the links on the editing page, it does not appear that way on the actual page that shows. You actually have to have an empty line between each line if you just want them to appear as a list. However, using a bulleted or numbered list works even better.

You asked: "Hello Dr. Fitzpatrick While at Auburn, did you become a big fan of the football team? If so, do you still follow them today?"

My answer: My dad went to Auburn, as well, so I grew up an Auburn fan. Being there on game day was an experience. 25000 residents of the town, with a stadium that seats 80000. In five years getting my bachelor's and master's degrees, I missed one home game. I saw Bo Jackson play (and Charles Barkley on the b-ball team). I was pretty excited with the recent national championship, and I am hoping Cam Newton will have a good pro career.